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(v2.1.1.9218) Fix unit tests
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@ -565,7 +565,7 @@ antibiogram.default <- function(x,
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# make list unique
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antimicrobials <- unique(user_ab)
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# go through list to set AMR in combinations
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for (i in seq_len(length(antimicrobials))) {
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for (i in seq_along(antimicrobials)) {
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abx <- antimicrobials[[i]]
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for (ab in abx) {
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# make sure they are SIR columns
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@ -896,7 +896,7 @@ antibiogram.default <- function(x,
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ab_naming_function <- function(x, t, l, s) {
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x <- strsplit(x, s, fixed = TRUE)
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out <- character(length = length(x))
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for (i in seq_len(length(x))) {
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for (i in seq_along(x)) {
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a <- x[[i]]
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if (is.null(t)) {
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# leave as is
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@ -941,7 +941,7 @@ antibiogram.default <- function(x,
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if (isTRUE(has_syndromic_group)) {
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grps <- unique(out$syndromic_group)
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for (i in seq_len(length(grps))) {
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for (i in seq_along(grps)) {
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grp <- grps[i]
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if (i == 1) {
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new_df <- long_to_wide(out[which(out$syndromic_group == grp), , drop = FALSE])
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4
R/sir.R
4
R/sir.R
@ -812,7 +812,7 @@ as.sir.data.frame <- function(x,
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x_mo <- as.mo(x[, col_mo, drop = TRUE])
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}
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for (i in seq_len(length(ab_cols))) {
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for (i in seq_along(ab_cols)) {
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if (types[i] == "mic") {
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x[, ab_cols[i]] <- x %pm>%
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pm_pull(ab_cols[i]) %pm>%
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@ -1621,7 +1621,7 @@ as_sir_method <- function(method_short,
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}
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notes <- unique(notes)
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if (isTRUE(verbose) || length(notes) == 1 || NROW(AMR_env$sir_interpretation_history) == 0) {
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for (i in seq_len(length(notes))) {
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for (i in seq_along(notes)) {
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message(word_wrap(" ", AMR_env$bullet_icon, " ", notes[i], add_fn = font_black))
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}
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} else {
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